Bad times for good bacteria: how modern life has damaged our internal ecosystems

Human actions damage ecosystems on a global scale. Our influence is so great we’ve triggered a new geological epoch, called the Anthropocene, simply because of the changes we’ve brought about. But it’s not just the outside environment we’ve changed, we’ve also damaged the ecosystems inside us.

Our activities alter natural processes, such as weather patterns, and the way nutrients, such as nitrogen and phosphorus, move within ecosystems. We cause declines in species diversity, trigger extinctions and introduce weeds and pests.

All this comes with costs, caused by the increasing unpredictability of both physical and biological systems. Our infrastructure and agriculture rely on a consistent climate, but that’s now becoming increasingly unreliable. And it’s not just the outside world that’s unpredictable; it may come as a surprise to some that we have internal ecosystems, and that these have also been damaged.

Shrinking population

Every adult is made up of 100 million, million human cells (that’s a one followed by 14 zeroes). But the human body is also home to ten times this number of bacterial cells, which, collectively, are called the microbiota. Biologists have only been exploring this internal ecosystem for a decade or so, but surprising and important results are already emerging.

Because the laboratory where I work is interested in how humans affect evolutionary processes, it was natural for us to ask how much humans might affect microbial ecosystems. The answer turns out to be quite a lot.

Possibly the most direct and personal effects are on our own microbiota. And these changes come with consequences for health and well-being. Exactly the same processes we see in external ecosystems – loss of diversity, extinction, and introduction of invasive species – are happening to our own microbiota. And damaged ecosystems don’t function as well as they should.

Scientists have tried to “go back in time” and ask what the original human microbiota might have looked like. There are three ways of doing this: biologists can look at the microbiota of our nearest relatives, the great apes; we can examine DNA from fossils; or we can look at the microbiota of modern-day humans who still have a hunter-gatherer lifestyle.

All these approaches tell the same story. Modern humans have a lower diversity of microbiota than our ancestors, and there’s been a consistent decline in this diversity across ancient and recent human history.

There are a number of reasons for the decline. The widespread use of fire from 350,000 years ago increased the calories we could obtain from food. This probably decreased our need for a big gut, and a smaller gut means less room for microbes.

The invention of agriculture between 8,000 and 10,000 years ago changed our diet, and with it, our microbiota. The end result was the extinction of some components of the microbiota in farming populations. Even today, hunter-gatherers and subsistence societies have many bacterial species in their gut that are never found in the guts of people from westernised societies.

One of the last hunter-gatherer societies in the world, the Yanomami people of South America, have a highly diverse and stable microbiota, and don’t suffer from diseases common in the developed world. christian caron/Flickr, CC BY-ND

Modern onslaught

Changes in microbiota have been tracked using bacteria preserved on the teeth of skeletons, and this showed falls in diversity linked to dietary changes, as well as a shift to microbial species associated with disease.

The changes are particularly apparent after the Industrial Revolution, when processed flour and sugar became widely available. And diet continues to have a major influence on our microbiota.

But the greatest disruption probably happened after the 1950s. This time period corresponds to a number of changes that directly affect the composition of the human microbiota. One involves the opportunity for microbiota to colonise newborns and infants. Normally, babies obtain some microbiota from their mother during childbirth, but caesarean births interrupt this opportunity. Bottle feeding, increased sanitation, and eating processed, sterile foods also limit opportunities to acquire microbiota.

Modern medicine has been very successful at controlling bacterial diseases with antibiotics. Unfortunately, antibiotics cause considerable collateral damage to innocent and beneficial bacteria. After antibiotic therapy, the microbiota may never return to their original abundance, and genetic diversity is reduced in those bacteria that remain.

Antibiotics can also damage beneficial bacteria. Photo: Shutterstock

Collectively, these changes mean that our microbial ecosystems have become degraded, much like natural ecosystems globally. The microbiota are less functional and resilient than they should be. And it turns out they have essential roles in developing our immune systems, and in regulating metabolism. So it shouldn’t be surprising that altered microbiota are now being associated with many diseases of the modern world.

These diseases include obesity, allergic reactions, chronic inflammatory conditions and autoimmune disorders. More recently, it’s also been suggested that psychological conditions, such as depression and anxiety, are linked to the bacteria that live inside us.

In some cases, the parallels with more conventional ecosystems are clear. Clostridium difficile is a bacterium that can grow out of control in our gut, like an invasive weed. And, like a weed invading degraded land, it often spreads rapidly after other bacteria have been eliminated from the gut by antibiotics. The most effective cure is similar to bush regeneration; donating microbiota from healthy volunteers (a “poo transplant”) helps restore a healthy ecosystem.

But, for many diseases associated with our microbiota, there are no immediate cures. Like most ecosystems, our gut bacteria are complex and dynamic. The challenge now is to understand this system and how to acquire and maintain a healthy microbiota, so that in the future, a microbiota check-up might be a routine part of a visit to the doctor.

In such a future, hunter-gatherers such as the Yanomami of the Amazon may turn out to be the custodians of valuable species that are extinct in the microbiota of the developed world.